BMRB Entry 17088

Name: Solution structure of the pseudouridine modified P6.1 hairpin of human telomerase RNA
Published: 2010-08-18

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PDB ID: 2kye
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17088
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Solution structure of the pseudouridine modified P6.1 hairpin of human telomerase RNA PubMed: 20554853

Deposition date: 2010-07-29 Original release date: 2010-08-18

Authors: Kim, Nak-Kyoon; Theimer, Carla; Mitchell, James; Collins, Kathleen; Feigon, Juli

Citation: Kim, Nak-Kyoon; Theimer, Carla; Mitchell, James; Collins, Kathleen; Feigon, Juli. "Effect of pseudouridylation on the structure and activity of the catalytically essential P6.1 hairpin in human telomerase RNA." Nucleic Acids Res. 38, 6746-6756 (2010).

Assembly members:
RNA, polymer, 15 residues, 4824.931 Da.

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source: Production method: enzymatic semisynthesis

Entity Sequences (FASTA):
RNA: GAGAGXXGGGCXCXC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	91
15N chemical shifts	16
1H chemical shifts	138

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	P6.1 hairpin	1

Entities:

Entity 1, P6.1 hairpin 15 residues - 4824.931 Da.

1

G

A

G

A

G

PSU

G

2

C

PSU

C

PSU

C

Samples:

Unlabeled_HDO: RNA 0.6 mM; H2O 95%; D2O 5%

Unlabeled_D2O: RNA 0.6 mM; D2O 100%

ACG_labeled_HDO: RNA, [U-98% 13C; U-98% 15N], 0.8 mM; H2O 95%; D2O 5%

ACG_labeled_D2O: RNA, [U-98% 13C; U-98% 15N], 0.8 mM; D2O 100%

HDO: ionic strength: 5 mM; pH: 6.8; pressure: 1 atm; temperature: 283 K

D2O: ionic strength: 5 mM; pH: 6.8; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	ACG_labeled_HDO	isotropic	HDO
2D 1H-13C HSQC	Unlabeled_D2O	isotropic	D2O
2D 1H-13C HSQC	ACG_labeled_D2O	isotropic	D2O
2D 1H-1H COSY	ACG_labeled_D2O	isotropic	D2O
2D 1H-1H NOESY	Unlabeled_HDO	isotropic	HDO
2D 1H-1H NOESY	Unlabeled_D2O	isotropic	D2O
2D 1H-1H Filter/Edited NOESY	ACG_labeled_D2O	isotropic	D2O
3D HCCH-TOCSY	ACG_labeled_D2O	isotropic	D2O
2D 1H-1H TOCSY	Unlabeled_HDO	isotropic	HDO
2D 1H-1H TOCSY	Unlabeled_D2O	isotropic	D2O

Software:

X-PLOR NIH v2.9.8, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

Molmol, Koradi, Billeter and Wuthrich - data analysis

xwinnmr, Bruker Biospin - collection, data analysis, processing

SPARKY, Goddard - chemical shift assignment, data analysis, peak picking

NMR spectrometers:

Bruker DRX 500 MHz
Bruker Avance 500 MHz
Bruker Avance 600 MHz
Bruker Avance 800 MHz